Beta_diversity_rumen
Chiara Gini
20/12/2021
Beta diversity analysis of samples of ruminal liquid of 4 animals (collected at the sloather house): I1, I2, I3 and I4. Control group consists in ruminal liquid + diet, treatments consist of control and AE1, AE sintethyc 1, Carvacrol, p-cymene, gamma-terpinene.
Comparison 1) Beta diversity: RUMINAL LIQUID VS CONTROL (RUMINAL LIQUID +DIET)
Between-sample variability from 16S rRna-gene sequencing data.
Clustering
PCA
Clustering by treatment (PCA) - ruminal liquid & control:
MDS
Clustering by treatment (MDS): NMDS1 vs NMDS2
## Warning in metaMDS(matx0, k = 3): stress is (nearly) zero: you may have
## insufficient data
Clustering by type (MDS): NMDS1 vs NMDS3
Clustering by type (MDS): NMDS2 vs NMDS3
Clustering by treatment by timepoint (MDS):
Significance of between-group distances
Significance values based on permuted analysis of variance (999 permutations), repeated 100 times.
- between treatments: p-value = 0.38205 (std = 0.0146587)
Below the ANOVA table from the model:
\[ X = \mu + treatment + timepoint + treatment*type + e \]
| Df | SumsOfSqs | MeanSqs | F.Model | R2 | Pr(>F) | |
|---|---|---|---|---|---|---|
| treatment | 1 | 0.0099243 | 0.0099243 | 0.8717938 | 0.0801886 | 0.381 |
| residuals | 10 | 0.1138372 | 0.0113837 | NA | 0.9198114 | NA |
| total | 11 | 0.1237615 | NA | NA | 1.0000000 | NA |
Going 3D
## Run 0 stress 0.008349506
## Run 1 stress 0.008361132
## ... Procrustes: rmse 0.0006056323 max resid 0.001177857
## ... Similar to previous best
## Run 2 stress 0.009198531
## Run 3 stress 0.009486074
## Run 4 stress 0.008528749
## ... Procrustes: rmse 0.007940972 max resid 0.01444052
## Run 5 stress 0.009099832
## Run 6 stress 0.008400782
## ... Procrustes: rmse 0.002416866 max resid 0.003687478
## ... Similar to previous best
## Run 7 stress 0.009092253
## Run 8 stress 0.008305532
## ... New best solution
## ... Procrustes: rmse 0.004207716 max resid 0.008817356
## ... Similar to previous best
## Run 9 stress 0.009205873
## Run 10 stress 0.01937812
## Run 11 stress 0.01941995
## Run 12 stress 0.009193597
## Run 13 stress 0.01960857
## Run 14 stress 0.01973618
## Run 15 stress 0.008418068
## ... Procrustes: rmse 0.005612771 max resid 0.008920026
## Run 16 stress 0.00919722
## Run 17 stress 0.009201285
## Run 18 stress 0.01946978
## Run 19 stress 0.008314335
## ... Procrustes: rmse 0.00114829 max resid 0.002707772
## ... Similar to previous best
## Run 20 stress 0.009197261
## *** Solution reachedComparison 2) Beta diversity: CONTROL VS TREATMENTS (control and treatments have all the same base of ruminal liquid+diet)
Between-sample variability from 16S rRna-gene sequencing data.
Clustering
PCA
Clustering by timepoint (PCA), removing ruminal liquid samples (I1 to I4):
Clustering by treatment (PCA)
MDS
Clustering by treatment (MDS): NMDS1 vs NMDS2
Clustering by type (MDS): NMDS1 vs NMDS3
Clustering by type (MDS): NMDS2 vs NMDS3
Clustering by treatment by timepoint (MDS):
Significance of between-group distances
Significance values based on permuted analysis of variance (999 permutations), repeated 100 times.
Between treatments: p-value = 0.95323 (std = 0.0073304)
Below the ANOVA table from the model:
\[ X = \mu + treatment + timepoint + treatment*type + e \]
| Df | SumsOfSqs | MeanSqs | F.Model | R2 | Pr(>F) | |
|---|---|---|---|---|---|---|
| treatment | 5 | 0.0433895 | 0.0086779 | 0.4765167 | 0.0536828 | 0.957 |
| residuals | 42 | 0.7648664 | 0.0182111 | NA | 0.9463172 | NA |
| total | 47 | 0.8082558 | NA | NA | 1.0000000 | NA |
going 3D
## Run 0 stress 0.01298168
## Run 1 stress 0.01343476
## ... Procrustes: rmse 0.005814629 max resid 0.03097529
## Run 2 stress 0.01305155
## ... Procrustes: rmse 0.001694783 max resid 0.004779158
## ... Similar to previous best
## Run 3 stress 0.01321474
## ... Procrustes: rmse 0.004034552 max resid 0.01080194
## Run 4 stress 0.01298176
## ... Procrustes: rmse 6.156712e-05 max resid 9.928578e-05
## ... Similar to previous best
## Run 5 stress 0.01298313
## ... Procrustes: rmse 0.0003468209 max resid 0.0005708492
## ... Similar to previous best
## Run 6 stress 0.0137477
## Run 7 stress 0.01298363
## ... Procrustes: rmse 0.0003651463 max resid 0.0005339837
## ... Similar to previous best
## Run 8 stress 0.01299097
## ... Procrustes: rmse 0.0009828238 max resid 0.001699637
## ... Similar to previous best
## Run 9 stress 0.01302572
## ... Procrustes: rmse 0.002387891 max resid 0.004365122
## ... Similar to previous best
## Run 10 stress 0.01346863
## ... Procrustes: rmse 0.004861004 max resid 0.01296442
## Run 11 stress 0.01298465
## ... Procrustes: rmse 0.0003201583 max resid 0.0005145715
## ... Similar to previous best
## Run 12 stress 0.01344956
## ... Procrustes: rmse 0.005961833 max resid 0.02966442
## Run 13 stress 0.01298693
## ... Procrustes: rmse 0.0007027888 max resid 0.001185948
## ... Similar to previous best
## Run 14 stress 0.01345628
## ... Procrustes: rmse 0.006062346 max resid 0.03015098
## Run 15 stress 0.01343369
## ... Procrustes: rmse 0.005813414 max resid 0.03124598
## Run 16 stress 0.01343993
## ... Procrustes: rmse 0.005859207 max resid 0.03043586
## Run 17 stress 0.01299213
## ... Procrustes: rmse 0.001041224 max resid 0.001821031
## ... Similar to previous best
## Run 18 stress 0.01298161
## ... New best solution
## ... Procrustes: rmse 7.462513e-05 max resid 0.0001719395
## ... Similar to previous best
## Run 19 stress 0.01343873
## ... Procrustes: rmse 0.005871508 max resid 0.03123103
## Run 20 stress 0.01298691
## ... Procrustes: rmse 0.0007380376 max resid 0.001210857
## ... Similar to previous best
## *** Solution reached